Back to Multiple platform build/check report for BioC 3.8
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BEclear on tokay1

This page was generated on 2019-04-13 11:25:23 -0400 (Sat, 13 Apr 2019).

Package 118/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 1.14.0
David Rasp
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/BEclear
Branch: RELEASE_3_8
Last Commit: e124e81
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BEclear
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BEclear_1.14.0.tar.gz
StartedAt: 2019-04-13 00:42:24 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:49:12 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 407.7 seconds
RetCode: 0
Status:  OK  
CheckDir: BEclear.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BEclear_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BEclear.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BEclear/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEclear' version '1.14.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BEclear' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
BEclear-package      0.50   0.05   16.83
correctBatchEffect   0.35   0.01   16.71
imputeMissingData    0.13   0.05   16.06
clearBEgenes         0.12   0.05   11.14
calcSummary          0.08   0.06   10.61
countValuesToPredict 0.13   0.00   11.25
calcScore            0.10   0.02   11.16
calcPvalues          0.10   0.01    6.17
makeBoxplot          0.07   0.03   11.48
calcMedians          0.04   0.00    6.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
BEclear-package      0.63   0.02   17.77
correctBatchEffect   0.45   0.05   19.16
imputeMissingData    0.16   0.04   17.50
clearBEgenes         0.17   0.00   12.81
makeBoxplot          0.17   0.00   11.00
countValuesToPredict 0.13   0.01   11.49
calcSummary          0.11   0.02   11.56
calcMedians          0.10   0.01    5.33
calcScore            0.06   0.03   10.84
calcPvalues          0.07   0.00    6.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

BEclear.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BEclear_1.14.0.tar.gz && rm -rf BEclear.buildbin-libdir && mkdir BEclear.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEclear.buildbin-libdir BEclear_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BEclear_1.14.0.zip && rm BEclear_1.14.0.tar.gz BEclear_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  192k  100  192k    0     0  5115k      0 --:--:-- --:--:-- --:--:-- 5670k

install for i386

* installing *source* package 'BEclear' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: BEclear
*** installing help indices
  converting help for package 'BEclear'
    finding HTML links ... done
    BEclear-example-methylation-data        html  
    BEclear-example-sample-data             html  
    BEclear-package                         html  
    calcBlockFrame                          html  
    calcMedians                             html  
    calcMediansForBatch                     html  
    calcPositions                           html  
    calcPvalsForBatch                       html  
    calcPvalues                             html  
    calcScore                               html  
    calcSummary                             html  
    clearBEgenes                            html  
    combineBlocks                           html  
    correctBatchEffect                      html  
    countValuesToPredict                    html  
    dlossp                                  html  
    ex.corrected.data                       html  
    findWrongValues                         html  
    gdepoch                                 html  
    imputeMissingData                       html  
    imputeMissingDataForBlock               html  
    loss                                    html  
    makeBoxplot                             html  
    nnz                                     html  
    replaceWrongValues                      html  
    runGradientDescent                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BEclear' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEclear' as BEclear_1.14.0.zip
* DONE (BEclear)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BEclear' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

BEclear.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BEclear)
Loading required package: BiocParallel
> 
> test_check("BEclear")
INFO [2019-04-13 00:48:29] Calculating the medians for 2 batches
INFO [2019-04-13 00:48:32] Calculating the medians for 3 batches
INFO [2019-04-13 00:48:37] Calculating the p-values for 2 batches
INFO [2019-04-13 00:48:40] Calculating the p-values for 3 batches
INFO [2019-04-13 00:48:43] Calculating the p-values for 3 batches
INFO [2019-04-13 00:48:47] Adjusting p-values
INFO [2019-04-13 00:48:47] 3 wrong values found
INFO [2019-04-13 00:48:47] Replacing values below 0 or above 1:
INFO [2019-04-13 00:48:47] 3 values replaced
== testthat results  ===========================================================
OK: 71 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.62    0.12   20.51 

BEclear.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BEclear)
Loading required package: BiocParallel
> 
> test_check("BEclear")
INFO [2019-04-13 00:48:49] Calculating the medians for 2 batches
INFO [2019-04-13 00:48:52] Calculating the medians for 3 batches
INFO [2019-04-13 00:48:57] Calculating the p-values for 2 batches
INFO [2019-04-13 00:49:00] Calculating the p-values for 3 batches
INFO [2019-04-13 00:49:04] Calculating the p-values for 3 batches
INFO [2019-04-13 00:49:08] Adjusting p-values
INFO [2019-04-13 00:49:08] 3 wrong values found
INFO [2019-04-13 00:49:08] Replacing values below 0 or above 1:
INFO [2019-04-13 00:49:08] 3 values replaced
== testthat results  ===========================================================
OK: 71 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.35    0.23   20.81 

Example timings

BEclear.Rcheck/examples_i386/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package 0.50 0.0516.83
calcMedians0.040.006.01
calcPvalues0.100.016.17
calcScore 0.10 0.0211.16
calcSummary 0.08 0.0610.61
clearBEgenes 0.12 0.0511.14
correctBatchEffect 0.35 0.0116.71
countValuesToPredict 0.13 0.0011.25
findWrongValues0.290.000.30
imputeMissingData 0.13 0.0516.06
makeBoxplot 0.07 0.0311.48
replaceWrongValues0.280.000.28

BEclear.Rcheck/examples_x64/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package 0.63 0.0217.77
calcMedians0.100.015.33
calcPvalues0.070.006.47
calcScore 0.06 0.0310.84
calcSummary 0.11 0.0211.56
clearBEgenes 0.17 0.0012.81
correctBatchEffect 0.45 0.0519.16
countValuesToPredict 0.13 0.0111.49
findWrongValues0.420.020.43
imputeMissingData 0.16 0.0417.50
makeBoxplot 0.17 0.0011.00
replaceWrongValues0.470.020.48